Research workbench
Crystal structure of putative glycoside hydrolase (YP_001304622.1) from parabacteroides distasonis atcc 8503 at 1.85 a resolution
Analyse Crystal structure of putative glycoside hydrolase (YP_001304622.1) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GYC
- Type
- protein
- Length
- 762 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative glycoside hydrolase
- UniProt
- A6LH36
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative glycoside hydrolase | protein | 381 | 45% helix, 11% strand | A6LH36 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 670 | 0.78 | 0.83 | 63 | EDO |
| 2 | 203 | 0.64 | 0.83 | 33 | empty |
| 3 | 150 | 0.63 | 0.85 | 25 | empty |
| 4 | 94 | 0.34 | 0.74 | 18 | EDO |
| 5 | 80 | 0.31 | 0.73 | 18 | EDO |
Interfaces
1 interface between chains.
- A–B · 1052 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3GYC · Crystal structure of putative glycoside hydrolase (YP_001304622.1) from Parabacteroides… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A6LH36
- Elsewhere: RCSB PDB 3GYC · PDBe 3GYC · UniProt A6LH36
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